Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1517 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0137855094 sf0137854051 1 37855094 1.86E-186 4.49E-29
vg0133382267 sf0133381223 1 33382267 4.93E-144 NA
vg1114200135 sf1113736456 11 14200135 8.79E-139 NA
vg0107563270 sf0107562270 1 7563270 1.20E-138 NA
vg0626576848 sf0626575851 6 26576848 1.75E-137 NA
vg0134540544 sf0134539501 1 34540544 8.31E-137 4.16E-08
vg0137836018 sf0137834975 1 37836018 NA 2.96E-29
vg0137799856 sf0137798813 1 37799856 NA 1.50E-10
vg0137829682 sf0137828639 1 37829682 NA 1.70E-10
vg1120474541 sf1120008466 11 20474541 NA 9.24E-09
vg0822896046 sf0822893333 8 22896046 NA 3.42E-08
vg1122046514 sf1121580385 11 22046514 NA 1.66E-07
vg0107608673 sf0107607673 1 7608673 NA 2.22E-07
vg0608024602 sf0608023603 6 8024602 NA 2.23E-07
vg1017105232 sf1017034004 10 17105232 NA 2.36E-07
vg0417539277 sf0417367319 4 17539277 NA 4.90E-07
vg0524272956 sf0524210375 5 24272956 NA 7.69E-07
vg0727490819 sf0727489825 7 27490819 NA 1.00E-06
vg0138183984 sf0138182941 1 38183984 NA 1.08E-06
vg1016997474 sf1016926246 10 16997474 NA 1.40E-06
vg0529535497 sf0529472852 5 29535497 NA 1.42E-06
vg0127954494 sf0127953450 1 27954494 NA 1.71E-06
vg0309822359 sf0309821295 3 9822359 NA 3.26E-06
vg0227953507 sf0227947638 2 27953507 NA 3.74E-06
vg0219802631 sf0219796763 2 19802631 NA 6.99E-06